VariantQuantileThresholding_Combined: VariantQuantileThresholding_Combined

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

VariantQuantileThresholding_Combined

Description

We get variants of interest using the quantile thresholding. This function combines the functions VariantSelection_Quantile, VariantSelection_Group and VariantSelection_TopCells. If you use top_cells and top_VAF, you have to only supply one quantil value (quantiles = 0.9, thresholds = 0). This function is adapted from the Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021

Usage

VariantQuantileThresholding_Combined(
  SE,
  min_coverage = 2,
  quantiles = c(0.1, 0.9),
  thresholds = c(0.1, 0.9),
  top_cells = NULL,
  top_VAF = NULL,
  min_quality = NULL,
  mean_allele_frequency = 0,
  group_of_interest = NULL,
  group1 = NULL,
  group2 = NULL,
  group_factor = NULL,
  remove_nocall = TRUE,
  verbose = TRUE
)

Arguments

SE	SummarizedExperiment object.
min_coverage	Minimum coverage needed.
quantiles	The lower and upper quantile you want to use.
thresholds	The VAF thresholds you want to use for the quantiles.
top_cells	The number of cells with at least top_VAF percent for a variant.
top_VAF	The VAF for the top cells.
min_quality	The minimum quality you want for the Variants of Interest. Can be ignored by setting it to NULL.
mean_allele_frequency	The minimum mean allele frequency. Default = 0
group_of_interest	The column data that divides the cells.
group1	The first group of interest. If set, the quantiles are only calculated for this group.
group2	The second group of interest.
group_factor	How much higher has the mean allele frequency to be in group 1 when compared to group 2?
remove_nocall	Should NoCall cells (consensus = 0) be disregarded during the analysis?
verbose	Should the function be verbose? Default = TRUE

CostaLab/sigurd documentation built on Feb. 10, 2025, 11:08 p.m.